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Adds Flag Variables for an Occurred Event .

Source: R/derive_vars_event_flag.R
derive_vars_event_flag.Rd

Creates two flag variables for the event occurred, one for the event occurred within each by group and one to flag if the event occurred or not for each day.

Usage

derive_vars_event_flag(
  dataset,
  by_vars,
  aval_cutoff,
  new_var1 = NULL,
  new_var2 = NULL
)

Arguments

dataset

Input dataset

The variables specified by the by_vars argument are expected.

by_vars

Grouping variables

The variables to be considered for grouping for creating a new variable new_var1

aval_cutoff

Cutoff value for AVAL

For TESTCD code list values based on diameter, if AVAL is greater than aval_cutoff then the event is considered to have occurred. For example, if aval_cutoff = 2.5 then the subjects with AVAL value greater than 2.5 are considered.

new_var1

Name of the new flag variable 1

A new flag variable will be created with values `Y` or `N`.
If the event is occurred at least once during a observation period for
a subject then the new variable will be flagged as `Y` otherwise `N`.

new_var2

Name of the new flag variable 2.

A new flag variable will be created with values `Y` or `N`.
If the event is occurred on the particular day then the new variable will
be flagged as `Y` otherwise `N`.

Value

The dataset with the flag variables added to it.

Details

The event is considered to have occurred if AVAL is greater than the aval_cutoff or AVALC has values Y, MILD, MODERATE, SEVERE. In all other cases, the event is not considered to have occurred.

The names for the new flag variables created will be sponsor specific.

For the new_var1 it will flag all observations as "Y" within the by group if the event occurred at least once during observation period. If the event is not at all occurred during the observation period then all the observations within by group will be flagged as "N".

For derived maximum records in FATESTCD , the new_var2 will be set to NA.

If both new_var1 and new_var2 are NULL, this function will return the input dataset as output dataset.

See also

Other der_var: derive_var_aval_adis(), derive_vars_crit(), derive_vars_max_flag(), derive_vars_merged_vaccine(), derive_vars_params(), derive_vars_vaxdt()

Examples

library(tibble)
library(admiral)
library(dplyr)

input <- tribble(
  ~USUBJID, ~FAOBJ, ~ATPTREF, ~AVAL, ~AVALC, ~FATEST, ~FATESTCD, ~FASCAT,
  "1", "REDNESS", "VAC1", 3.5, "3.5", "Diameter", "DIAMETER", "ADMIN-SITE",
  "1", "REDNESS", "VAC1", 4.5, "4.5", "Diameter", "DIAMETER", "ADMIN-SITE",
  "1", "REDNESS", "VAC1", 1.5, "1.5", "Diameter", "DIAMETER", "ADMIN-SITE",
  "1", "REDNESS", "VAC1", 4.5, "4.5", "Diameter", "DIAMETER", "ADMIN-SITE",
  "1", "FATIGUE", "VAC1", 1, "MILD", "Severity", "SEV", "SYSTEMIC",
  "1", "FATIGUE", "VAC1", 2, "MODERATE", "Severity", "SEV", "SYSTEMIC",
  "1", "FATIGUE", "VAC1", 0, "NONE", "Severity", "SEV", "SYSTEMIC",
  "1", "FATIGUE", "VAC1", 2, "MODERATE", "Severity", "SEV", "SYSTEMIC",
  "1", "REDNESS", "VAC2", 6.5, "6.5", "Diameter", "DIAMETER", "ADMIN-SITE",
  "1", "REDNESS", "VAC2", 7.5, "7.5", "Diameter", "DIAMETER", "ADMIN-SITE",
  "1", "REDNESS", "VAC2", 2.5, "2.5", "Diameter", "DIAMETER", "ADMIN-SITE",
  "1", "REDNESS", "VAC2", 7.5, "7.5", "Diameter", "DIAMETER", "ADMIN-SITE",
  "1", "FATIGUE", "VAC2", 1, "MILD", "Severity", "SEV", "SYSTEMIC",
  "1", "FATIGUE", "VAC2", 2, "MODERATE", "Severity", "SEV", "SYSTEMIC",
  "1", "FATIGUE", "VAC2", 0, "NONE", "Severity", "SEV", "SYSTEMIC",
  "1", "FATIGUE", "VAC2", 2, "MODERATE", "Severity", "SEV", "SYSTEMIC",
)

derive_vars_event_flag(
  dataset = input,
  by_vars = exprs(USUBJID, FAOBJ, ATPTREF),
  aval_cutoff = 2.5,
  new_var1 = EVENTL,
  new_var2 = EVENTDL
)
#> # A tibble: 16 × 10
#>    USUBJID FAOBJ   ATPTREF  AVAL AVALC    FATEST  FATESTCD FASCAT EVENTL EVENTDL
#>    <chr>   <chr>   <chr>   <dbl> <chr>    <chr>   <chr>    <chr>  <chr>  <chr>  
#>  1 1       REDNESS VAC1      3.5 3.5      Diamet… DIAMETER ADMIN… Y      Y      
#>  2 1       REDNESS VAC1      4.5 4.5      Diamet… DIAMETER ADMIN… Y      Y      
#>  3 1       REDNESS VAC1      1.5 1.5      Diamet… DIAMETER ADMIN… Y      N      
#>  4 1       REDNESS VAC1      4.5 4.5      Diamet… DIAMETER ADMIN… Y      Y      
#>  5 1       FATIGUE VAC1      1   MILD     Severi… SEV      SYSTE… Y      Y      
#>  6 1       FATIGUE VAC1      2   MODERATE Severi… SEV      SYSTE… Y      Y      
#>  7 1       FATIGUE VAC1      0   NONE     Severi… SEV      SYSTE… Y      N      
#>  8 1       FATIGUE VAC1      2   MODERATE Severi… SEV      SYSTE… Y      Y      
#>  9 1       REDNESS VAC2      6.5 6.5      Diamet… DIAMETER ADMIN… Y      Y      
#> 10 1       REDNESS VAC2      7.5 7.5      Diamet… DIAMETER ADMIN… Y      Y      
#> 11 1       REDNESS VAC2      2.5 2.5      Diamet… DIAMETER ADMIN… Y      N      
#> 12 1       REDNESS VAC2      7.5 7.5      Diamet… DIAMETER ADMIN… Y      Y      
#> 13 1       FATIGUE VAC2      1   MILD     Severi… SEV      SYSTE… Y      Y      
#> 14 1       FATIGUE VAC2      2   MODERATE Severi… SEV      SYSTE… Y      Y      
#> 15 1       FATIGUE VAC2      0   NONE     Severi… SEV      SYSTE… Y      N      
#> 16 1       FATIGUE VAC2      2   MODERATE Severi… SEV      SYSTE… Y      Y